@JoshRoss: Oh, what a horrible game! Wasn't that the first DirectX game?
I don't think so - DirectX was released after Windows 95, but Hover! was included in the Windows 95 CD. Windows did support a few other game APIs, like WinG so it's not like the game was done with GDI.
But Hover doesn't match the OP's description - it does have hovercraft and has you collecting flags, but its a first-person game with real-time control and doesn't have any customizable loadouts beyond collectable powerups.